from ctypes import * from ctypes.util import find_library from os import path from glob import glob import sys from enum import IntEnum try: import numpy as np import scipy from scipy import sparse except: scipy = None if sys.version_info[0] < 3: range = xrange from itertools import izip as zip __all__ = ['liblinear', 'feature_node', 'gen_feature_nodearray', 'problem', 'parameter', 'model', 'toPyModel', 'solver_names', 'print_null'] try: dirname = path.dirname(path.abspath(__file__)) dynamic_lib_name = 'clib.cp*' path_to_so = glob(path.join(dirname, dynamic_lib_name))[0] liblinear = CDLL(path_to_so) except: try : if sys.platform == 'win32': liblinear = CDLL(path.join(dirname, r'..\..\windows\liblinear.dll')) else: liblinear = CDLL(path.join(dirname, '../../liblinear.so.6')) except: # For unix the prefix 'lib' is not considered. if find_library('linear'): liblinear = CDLL(find_library('linear')) elif find_library('liblinear'): liblinear = CDLL(find_library('liblinear')) else: raise Exception('LIBLINEAR library not found.') class solver_names(IntEnum): L2R_LR = 0 L2R_L2LOSS_SVC_DUAL = 1 L2R_L2LOSS_SVC = 2 L2R_L1LOSS_SVC_DUAL = 3 MCSVM_CS = 4 L1R_L2LOSS_SVC = 5 L1R_LR = 6 L2R_LR_DUAL = 7 L2R_L2LOSS_SVR = 11 L2R_L2LOSS_SVR_DUAL = 12 L2R_L1LOSS_SVR_DUAL = 13 ONECLASS_SVM = 21 PRINT_STRING_FUN = CFUNCTYPE(None, c_char_p) def print_null(s): return # In multi-threading, all threads share the same memory space of # the dynamic library (liblinear). Thus, we use a module-level # variable to keep a reference to ctypes print_null, preventing # python from garbage collecting it in thread B while thread A # still needs it. Check the usage of svm_set_print_string_function() # in LIBLINEAR README for details. ctypes_print_null = PRINT_STRING_FUN(print_null) def genFields(names, types): return list(zip(names, types)) def fillprototype(f, restype, argtypes): f.restype = restype f.argtypes = argtypes class feature_node(Structure): _names = ["index", "value"] _types = [c_int, c_double] _fields_ = genFields(_names, _types) def __str__(self): return '%d:%g' % (self.index, self.value) def gen_feature_nodearray(xi, feature_max=None): if feature_max: assert(isinstance(feature_max, int)) xi_shift = 0 # ensure correct indices of xi if scipy and isinstance(xi, tuple) and len(xi) == 2\ and isinstance(xi[0], np.ndarray) and isinstance(xi[1], np.ndarray): # for a sparse vector index_range = xi[0] + 1 # index starts from 1 if feature_max: index_range = index_range[np.where(index_range <= feature_max)] elif scipy and isinstance(xi, np.ndarray): xi_shift = 1 index_range = xi.nonzero()[0] + 1 # index starts from 1 if feature_max: index_range = index_range[np.where(index_range <= feature_max)] elif isinstance(xi, (dict, list, tuple)): if isinstance(xi, dict): index_range = sorted(xi.keys()) elif isinstance(xi, (list, tuple)): xi_shift = 1 index_range = range(1, len(xi) + 1) index_range = list(filter(lambda j: xi[j-xi_shift] != 0, index_range)) if feature_max: index_range = list(filter(lambda j: j <= feature_max, index_range)) else: raise TypeError('xi should be a dictionary, list, tuple, 1-d numpy array, or tuple of (index, data)') ret = (feature_node*(len(index_range)+2))() ret[-1].index = -1 # for bias term ret[-2].index = -1 if scipy and isinstance(xi, tuple) and len(xi) == 2\ and isinstance(xi[0], np.ndarray) and isinstance(xi[1], np.ndarray): # for a sparse vector # since xi=(indices, values), we must sort them simultaneously. for idx, arg in enumerate(np.argsort(index_range)): ret[idx].index = index_range[arg] ret[idx].value = (xi[1])[arg] else: for idx, j in enumerate(index_range): ret[idx].index = j ret[idx].value = xi[j - xi_shift] max_idx = 0 if len(index_range) > 0: max_idx = index_range[-1] return ret, max_idx try: from numba import jit jit_enabled = True except: # We need to support two cases: when jit is called with no arguments, and when jit is called with # a keyword argument. def jit(func=None, *args, **kwargs): if func is None: # This handles the case where jit is used with parentheses: @jit(nopython=True) return lambda x: x else: # This handles the case where jit is used without parentheses: @jit return func jit_enabled = False @jit(nopython=True) def csr_to_problem_jit(l, x_val, x_ind, x_rowptr, prob_val, prob_ind, prob_rowptr): for i in range(l): b1,e1 = x_rowptr[i], x_rowptr[i+1] b2,e2 = prob_rowptr[i], prob_rowptr[i+1]-2 for j in range(b1,e1): prob_ind[j-b1+b2] = x_ind[j]+1 prob_val[j-b1+b2] = x_val[j] def csr_to_problem_nojit(l, x_val, x_ind, x_rowptr, prob_val, prob_ind, prob_rowptr): for i in range(l): x_slice = slice(x_rowptr[i], x_rowptr[i+1]) prob_slice = slice(prob_rowptr[i], prob_rowptr[i+1]-2) prob_ind[prob_slice] = x_ind[x_slice]+1 prob_val[prob_slice] = x_val[x_slice] def csr_to_problem(x, prob): if not x.has_sorted_indices: x.sort_indices() # Extra space for termination node and (possibly) bias term x_space = prob.x_space = np.empty((x.nnz+x.shape[0]*2), dtype=feature_node) # rowptr has to be a 64bit integer because it will later be used for pointer arithmetic, # which overflows when the added pointer points to an address that is numerically high. prob.rowptr = x.indptr.astype(np.int64, copy=True) prob.rowptr[1:] += 2*np.arange(1,x.shape[0]+1) prob_ind = x_space["index"] prob_val = x_space["value"] prob_ind[:] = -1 if jit_enabled: csr_to_problem_jit(x.shape[0], x.data, x.indices, x.indptr, prob_val, prob_ind, prob.rowptr) else: csr_to_problem_nojit(x.shape[0], x.data, x.indices, x.indptr, prob_val, prob_ind, prob.rowptr) class problem(Structure): _names = ["l", "n", "y", "x", "bias"] _types = [c_int, c_int, POINTER(c_double), POINTER(POINTER(feature_node)), c_double] _fields_ = genFields(_names, _types) def __init__(self, y, x, bias = -1): if (not isinstance(y, (list, tuple))) and (not (scipy and isinstance(y, np.ndarray))): raise TypeError("type of y: {0} is not supported!".format(type(y))) if isinstance(x, (list, tuple)): if len(y) != len(x): raise ValueError("len(y) != len(x)") elif scipy != None and isinstance(x, (np.ndarray, sparse.spmatrix)): if len(y) != x.shape[0]: raise ValueError("len(y) != len(x)") if isinstance(x, np.ndarray): x = np.ascontiguousarray(x) # enforce row-major if isinstance(x, sparse.spmatrix): x = x.tocsr() pass else: raise TypeError("type of x: {0} is not supported!".format(type(x))) self.l = l = len(y) self.bias = -1 max_idx = 0 x_space = self.x_space = [] if scipy != None and isinstance(x, sparse.csr_matrix): csr_to_problem(x, self) max_idx = x.shape[1] else: for i, xi in enumerate(x): tmp_xi, tmp_idx = gen_feature_nodearray(xi) x_space += [tmp_xi] max_idx = max(max_idx, tmp_idx) self.n = max_idx self.y = (c_double * l)() if scipy != None and isinstance(y, np.ndarray): np.ctypeslib.as_array(self.y, (self.l,))[:] = y else: for i, yi in enumerate(y): self.y[i] = yi self.x = (POINTER(feature_node) * l)() if scipy != None and isinstance(x, sparse.csr_matrix): base = addressof(self.x_space.ctypes.data_as(POINTER(feature_node))[0]) x_ptr = cast(self.x, POINTER(c_uint64)) x_ptr = np.ctypeslib.as_array(x_ptr,(self.l,)) x_ptr[:] = self.rowptr[:-1]*sizeof(feature_node)+base else: for i, xi in enumerate(self.x_space): self.x[i] = xi self.set_bias(bias) def set_bias(self, bias): if self.bias == bias: return if bias >= 0 and self.bias < 0: self.n += 1 node = feature_node(self.n, bias) if bias < 0 and self.bias >= 0: self.n -= 1 node = feature_node(-1, bias) if isinstance(self.x_space, list): for xi in self.x_space: xi[-2] = node else: self.x_space["index"][self.rowptr[1:]-2] = node.index self.x_space["value"][self.rowptr[1:]-2] = node.value self.bias = bias def copy(self): prob_copy = problem.__new__(problem) for key in problem._names + list(vars(self)): setattr(prob_copy, key, getattr(self, key)) return prob_copy class parameter(Structure): _names = ["solver_type", "eps", "C", "nr_weight", "weight_label", "weight", "p", "nu", "init_sol", "regularize_bias", "w_recalc"] _types = [c_int, c_double, c_double, c_int, POINTER(c_int), POINTER(c_double), c_double, c_double, POINTER(c_double), c_int,c_bool] _fields_ = genFields(_names, _types) def __init__(self, options = None): if options == None: options = '' self.parse_options(options) def __str__(self): s = '' attrs = parameter._names + list(self.__dict__.keys()) values = map(lambda attr: getattr(self, attr), attrs) for attr, val in zip(attrs, values): s += (' %s: %s\n' % (attr, val)) s = s.strip() return s def set_to_default_values(self): self.solver_type = solver_names.L2R_L2LOSS_SVC_DUAL self.eps = float('inf') self.C = 1 self.p = 0.1 self.nu = 0.5 self.nr_weight = 0 self.weight_label = None self.weight = None self.init_sol = None self.bias = -1 self.regularize_bias = 1 self.w_recalc = False self.flag_cross_validation = False self.flag_C_specified = False self.flag_p_specified = False self.flag_solver_specified = False self.flag_find_parameters = False self.nr_fold = 0 self.print_func = cast(None, PRINT_STRING_FUN) def parse_options(self, options): if isinstance(options, list): argv = options elif isinstance(options, str): argv = options.split() else: raise TypeError("arg 1 should be a list or a str.") self.set_to_default_values() self.print_func = cast(None, PRINT_STRING_FUN) weight_label = [] weight = [] i = 0 while i < len(argv) : if argv[i] == "-s": i = i + 1 self.solver_type = solver_names(int(argv[i])) self.flag_solver_specified = True elif argv[i] == "-c": i = i + 1 self.C = float(argv[i]) self.flag_C_specified = True elif argv[i] == "-p": i = i + 1 self.p = float(argv[i]) self.flag_p_specified = True elif argv[i] == "-n": i = i + 1 self.nu = float(argv[i]) elif argv[i] == "-e": i = i + 1 self.eps = float(argv[i]) elif argv[i] == "-B": i = i + 1 self.bias = float(argv[i]) elif argv[i] == "-v": i = i + 1 self.flag_cross_validation = 1 self.nr_fold = int(argv[i]) if self.nr_fold < 2 : raise ValueError("n-fold cross validation: n must >= 2") elif argv[i].startswith("-w"): i = i + 1 self.nr_weight += 1 weight_label += [int(argv[i-1][2:])] weight += [float(argv[i])] elif argv[i] == "-q": self.print_func = ctypes_print_null elif argv[i] == "-C": self.flag_find_parameters = True elif argv[i] == "-R": self.regularize_bias = 0 else: raise ValueError("Wrong options") i += 1 liblinear.set_print_string_function(self.print_func) self.weight_label = (c_int*self.nr_weight)() self.weight = (c_double*self.nr_weight)() for i in range(self.nr_weight): self.weight[i] = weight[i] self.weight_label[i] = weight_label[i] # default solver for parameter selection is L2R_L2LOSS_SVC if self.flag_find_parameters: if not self.flag_cross_validation: self.nr_fold = 5 if not self.flag_solver_specified: self.solver_type = solver_names.L2R_L2LOSS_SVC self.flag_solver_specified = True elif self.solver_type not in [solver_names.L2R_LR, solver_names.L2R_L2LOSS_SVC, solver_names.L2R_L2LOSS_SVR]: raise ValueError("Warm-start parameter search only available for -s 0, -s 2 and -s 11") if self.eps == float('inf'): if self.solver_type in [solver_names.L2R_LR, solver_names.L2R_L2LOSS_SVC]: self.eps = 0.01 elif self.solver_type in [solver_names.L2R_L2LOSS_SVR]: self.eps = 0.0001 elif self.solver_type in [solver_names.L2R_L2LOSS_SVC_DUAL, solver_names.L2R_L1LOSS_SVC_DUAL, solver_names.MCSVM_CS, solver_names.L2R_LR_DUAL]: self.eps = 0.1 elif self.solver_type in [solver_names.L1R_L2LOSS_SVC, solver_names.L1R_LR]: self.eps = 0.01 elif self.solver_type in [solver_names.L2R_L2LOSS_SVR_DUAL, solver_names.L2R_L1LOSS_SVR_DUAL]: self.eps = 0.1 elif self.solver_type in [solver_names.ONECLASS_SVM]: self.eps = 0.01 class model(Structure): _names = ["param", "nr_class", "nr_feature", "w", "label", "bias", "rho"] _types = [parameter, c_int, c_int, POINTER(c_double), POINTER(c_int), c_double, c_double] _fields_ = genFields(_names, _types) def __init__(self): self.__createfrom__ = 'python' def __del__(self): # free memory created by C to avoid memory leak if hasattr(self, '__createfrom__') and self.__createfrom__ == 'C': liblinear.free_and_destroy_model(pointer(self)) def get_nr_feature(self): return liblinear.get_nr_feature(self) def get_nr_class(self): return liblinear.get_nr_class(self) def get_labels(self): nr_class = self.get_nr_class() labels = (c_int * nr_class)() liblinear.get_labels(self, labels) return labels[:nr_class] def get_decfun_coef(self, feat_idx, label_idx=0): return liblinear.get_decfun_coef(self, feat_idx, label_idx) def get_decfun_bias(self, label_idx=0): return liblinear.get_decfun_bias(self, label_idx) def get_decfun_rho(self): return liblinear.get_decfun_rho(self) def get_decfun(self, label_idx=0): w = [liblinear.get_decfun_coef(self, feat_idx, label_idx) for feat_idx in range(1, self.nr_feature+1)] if self.is_oneclass_model(): rho = self.get_decfun_rho() return (w, -rho) else: b = liblinear.get_decfun_bias(self, label_idx) return (w, b) def is_probability_model(self): return (liblinear.check_probability_model(self) == 1) def is_regression_model(self): return (liblinear.check_regression_model(self) == 1) def is_oneclass_model(self): return (liblinear.check_oneclass_model(self) == 1) def toPyModel(model_ptr): """ toPyModel(model_ptr) -> model Convert a ctypes POINTER(model) to a Python model """ if bool(model_ptr) == False: raise ValueError("Null pointer") m = model_ptr.contents m.__createfrom__ = 'C' return m fillprototype(liblinear.train, POINTER(model), [POINTER(problem), POINTER(parameter)]) fillprototype(liblinear.find_parameters, None, [POINTER(problem), POINTER(parameter), c_int, c_double, c_double, POINTER(c_double), POINTER(c_double), POINTER(c_double)]) fillprototype(liblinear.cross_validation, None, [POINTER(problem), POINTER(parameter), c_int, POINTER(c_double)]) fillprototype(liblinear.predict_values, c_double, [POINTER(model), POINTER(feature_node), POINTER(c_double)]) fillprototype(liblinear.predict, c_double, [POINTER(model), POINTER(feature_node)]) fillprototype(liblinear.predict_probability, c_double, [POINTER(model), POINTER(feature_node), POINTER(c_double)]) fillprototype(liblinear.save_model, c_int, [c_char_p, POINTER(model)]) fillprototype(liblinear.load_model, POINTER(model), [c_char_p]) fillprototype(liblinear.get_nr_feature, c_int, [POINTER(model)]) fillprototype(liblinear.get_nr_class, c_int, [POINTER(model)]) fillprototype(liblinear.get_labels, None, [POINTER(model), POINTER(c_int)]) fillprototype(liblinear.get_decfun_coef, c_double, [POINTER(model), c_int, c_int]) fillprototype(liblinear.get_decfun_bias, c_double, [POINTER(model), c_int]) fillprototype(liblinear.get_decfun_rho, c_double, [POINTER(model)]) fillprototype(liblinear.free_model_content, None, [POINTER(model)]) fillprototype(liblinear.free_and_destroy_model, None, [POINTER(POINTER(model))]) fillprototype(liblinear.destroy_param, None, [POINTER(parameter)]) fillprototype(liblinear.check_parameter, c_char_p, [POINTER(problem), POINTER(parameter)]) fillprototype(liblinear.check_probability_model, c_int, [POINTER(model)]) fillprototype(liblinear.check_regression_model, c_int, [POINTER(model)]) fillprototype(liblinear.check_oneclass_model, c_int, [POINTER(model)]) fillprototype(liblinear.set_print_string_function, None, [CFUNCTYPE(None, c_char_p)])